Lysinibacillus sphaericus is one of the bacteria used as a bio-insecticide as part of vector control programs against tropical diseases, such as malaria, filariasis, yellow fever, dengue fever and West Nile virus [1]. L. sphaericus isolates may be classified according to their larvicidal activity into high and low toxicity strains. High- and low-toxicity strains synthesize mosquitocidal toxins (Mtx) in vegetative growth cells [2]. Highly toxic strains produce a binary toxin coded by binA and binB genes in sporulating stages [3]. In addition, L. sphaericus larvicidal toxicity may be explained due to expression of Cry48/Cry49 toxin [4] and the S-layer protein [5]. Vegetative and sporulated cells of L. sphaericus CBAM5 are pathogenic towards Culex quinquefasciatus larvae [6]. LC50 (50% lethal concentration) toward C. quinquefasciatus larvae of strain CBAM5 is 1400 cells/mL from sporulated cultures, being this isolate assigned as a high-toxicity strain [6].

The biotechnological application of L. sphaericus is not limited to biological control. L. sphaericus biomass has been applied in the bioremediation of heavy metals, such as cobalt, copper, chromium and lead [7] with specific metal binding in the cell surface [8]. Native Colombian isolates L. sphaericus OT4b.31 and IV(4)10 showed heavy metal biosorption in living and dead biomass, both strains expressing the S-layer proteins [9]. L. sphaericus strain CBAM5, along with other 24 native isolates, shown effective growth in arsenate, hexavalent chromium and/or lead [6, 10].

Considering that Lysinibacillus sphaericus CBAM5 is a relevant native strain, not only by its highly toxic larvicidal activity but also by its heavy metal tolerance, we have chosen this strain to analyze its genomic sequence. In this report, we present a summary classification, and set of general features for Lysinibacillus sphaericus strain CBAM5 including previously unreported aspects of its phenotype, together with the description of its genome sequence and annotation.

Organism information

Lysinibacillus sphaericus is an aerobic, mesophilic, spore-forming and Gram-positive bacterium, commonly isolated from soil and water [11]. Formerly known as Bacillus sphaericus, the species was later reassigned to the genus Lysinibacillus because of its distinctive peptidoglycan membrane composition, and physiological features [12, 13]. Lysinibacillus sphaericus strains have been classified into five DNA homology groups, where mosquito larvicidal strains were placed into DNA subgroup IIA [14] while the subgroup IIB was reclassified as Lysinibacillus fusiformis
[15]. Later, according to 16S rDNA and lipid profile comparisons, Lysinibacillus sphaericus strains were classified into seven similarity subgroups, of which only four retained the previous description by Krych et al. [15]. Groups VI and VII were later reclassified as new species [16]. Because of the phenotypic and genetic diversity summarized above, most of the groups remain designated as Lysinibacillus sphaericus sensu lato.

Partial 16S rRNA gene sequences (1,421 bp) were aligned to establish the phylogenetic neighborhood of Lysinibacillus sphaericus CBAM5 (Figure 1). The phylogenetic tree was constructed by using the Maximum Likelihood method on the Tamura-Nei model [17]. Initial tree for the heuristic search was obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach. Evolutionary analyses were conducted in MEGA6 [18]. The stability of relationships was assessed by bootstrap analysis based on 1,000 resamplings for the tree topology. L. sphaericus CBAM5 was assigned to the DNA similarity group 1 (formerly known as DNA homology group IIA), in line with a previous classification of mosquito pathogenic native strains [6].

aEvidence codes - IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [30].

Genome sequencing information

Genome project history

The genome sequencing of Lysinibacillus sphaericus CBAM5 was supported by the CIMIC (Centro de Investigaciones Microbiológicas) laboratory at the University of Los Andes within the Grant (1204-452-21129) of the Instituto Colombiano para el Fomento de la Investigación Francisco José de Caldas. Whole genomic DNA extraction and bioinformatics analysis was performed at CIMIC laboratory, whereas libraries construction and whole shotgun sequencing at the Beijing Genome Institute (BGI) Americas Laboratory (Tai Po, Hong Kong). The applied pipeline included quality check of reads, de novo assembly, a gap-filling step and mapping against a reference genome. This whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AYKQ00000000. The version described in this paper is the first version, AYKQ01000000. A summary of the project information is shown in Table 2.

Growth conditions and DNA isolation

Lysinibacillus sphaericus strain CBAM5 was grown in nutrient broth for 16 hours at 30°C and 150 rev/min. High molecular weight DNA was isolated using the EasyDNA® Kit (Carlsbad, CA, USA. Invitrogen) as indicated by the manufacturer. DNA purity and concentration were determined in a NanoDrop spectrophotometer (Wilmington, DE, USA. Thermo Scientific).

Genome sequencing and assembly

After DNA extraction, samples were sent to the Beijing Genome Institute (BGI) Americas Laboratory (Tai Po, Hong Kong). Purified DNA sample was first sheared into smaller fragments with a desired size by a Covaris E210 ultrasonicator. Then the overhangs resulting from fragmentation were converted into blunt ends by using T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase. After adding an “A” base to the 3’ end of the blunt phosphorylated DNA fragments, adapters were ligated to the ends of the DNA fragments. The desired fragments were purified though gel-electrophoresis, then selectively enriched and amplified by PCR. The index tag was introduced into the adapter at the PCR stage as appropriate, and a library quality test was performed. Lastly, qualified, short, paired-ends of 90:90 bp length with 500 bp insert libraries were used to cluster preparation and to conduct whole-shotgun sequencing in Illumina Hi-Seq 2000 sequencers.

Using the FASTX-Toolkit version 0.6.1 [31] and clean_reads version 0.2.3 from the ngs_backbone pipeline [32] reads were trimmed and quality filtered. Four preliminary assemblies were obtained by using: SOAPdenovo version 2.04 [33], Velvet version 1.2.10 [34], ABySS version 1.3.7 [35], and CLC Assembly Cell version 4.0.10 [36]. Those assemblies were integrated in the CISA pipeline resulting in a consensus assembly [37]. SOAPdenovo and CLC Assembly Cell packages included automatic scaffolding and k-mer/overlapping optimization steps. To obtain structural insight of a chromosomal scaffold, we used CONTIGuator.2 [38], using the Lysinibacillus sphaericus strain C3-41 chromosome (accession number: CP000817.1) as reference. Some gaps were successfully filled by using GapFiller [39]. Gap-filling steps were applied over each one of the preliminary assemblies and over the final consensus assembly. Quality assessment of the assembly was performed with iCORN [40]. The error rate of the final assembly is less than 1 in 1,000,000 bp. We compared the chromosomal assembly of L. sphaericus CBAM5 with the chromosome sequences of L. sphaericus C3-41 and L. sphaericus OT4b.31 by maximal unique matching of translated sequences with PROmer [41], and a read mapping single nucleotide polymorphism (SNP) effect analysis with SnpEff package [42].

Genome annotation

The Glimmer 3 gene finder was used to identify and extract sequences for potential coding regions. To achieve the functional annotation steps, the RAST server [43] and Blast2GO pipelines [44] were used. Blast2GO performed the blasting, GO-mapping and annotation steps; which included a description according to the ProDom, FingerPRINTScan, PIR-PSD, Pfam, TIRGfam, PROSITE, ProDom, SMART, SuperFamily, Pattern, Gene3D, PANTHER, SignalIP and TM-HMM databases. The results were summarized with InterPro [45]. Additionally, a GO-EnzymeCode mapping step was used to retrieve KEGG pathway-maps. tRNA genes were identified by using tRNAscan-SE [46] and rRNA genes by using RNAmmer [47]. The possible orthologs of the genome were identified based on the COG database and classified accordingly [48]. Prophage region prediction was also conducted by using the PHAST tool [49].

The genome summary and statistics are provided in Tables 3 and 4, and Figure 2. The genome consists of 60 scaffolds in 5,146,656 bp total size with a GC content of 37.19%. A total of 19 scaffolds were successfully aligned to a reference sequence, comprising 4,610,292 bp of sequence and are represented by the red and blue bars within the outer ring of Figure 2. Of the 5,620 genes predicted, 5,209 were protein-coding genes and 207 RNAs were identified. Genes assigned a putative function comprised 57.37% of the protein-coding genes while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 5.

Table 3

Summary of genome

Label

Size (bp)

Topology

INSDC identifier

Chromosomal scaffold

4,610,292

Circular

KK037167.1

Extrachromosomal elements

536,364

Linear

KK037168.1-KK037224.1

Table 4

Nucleotide content and gene count levels of the genome

Attribute

Value

% of total
a

Genome size (bp)

5,146,656

100.00

DNA GC content (bp)

1,913,947

37.19

DNA coding region (bp)

4,311,603

83.77

Number of replicons

1

Total genes

5,620

100

RNA genes

207

3.68

tRNA genes

180

3.20

Protein-coding genes

5,209

92.69

Genes in paralog clusters

151

2.69

Genes assigned to COGs

3701

65.85

1 or more conserved domains

2,520

44.84

2 or more conserved domains

834

14.84

3 or more conserved domains

361

6.42

Genes with function prediction

3,224

57.37

Genes assigned Pfam domains

3,995

71.09

Genes with signal peptides

459

8.17

Genes with transmembrane helices

1,140

20.28

CRISPR repeats

1

aThe total is based on either the size of the genome in base pairs or the total number of protein coding genes in the annotated genome.

We propose a 19-supercontig chromosomal scaffold of Lysinibacillus sphaericus CBAM5 with 4.61 Mbp in length, corresponding to a 99.4% of the reference chromosomal sequence. The remaining non-mapped or non-integrated contigs were aligned to plasmid reference sequences, leading to no significant coverage levels (data not shown). Then, we assigned those contigs as a set of potential extrachromosomal elements. Chromosomal comparison from the PROmer analysis between L. sphaericus strains CBAM5 and C3-41 showed that most of the two chromosomes mapped onto each other, revealing large segments of high similarity (Figure 3). In contrast, the comparison between the native strains L. sphaericus CBAM5 and OT4b.31 revealed scattered regions across the dot-plot, corresponding to low coverage levels and different synthenial arrangements. Only variants with a phred-scaled quality and depth coverage scores greater than 100 were considered valid for the SNV analysis. We found 378 variants corresponding to 4531 effects being classified as follows: 170 insertions, 280 deletions, 2020 downstream effects, 182 frame shifts, 211 intergenic effects, 2 start losts, 2 stop losts and 2114 upstream effects. In addition, no transitions, transversions, missense or silent effects were identified. As per most of the variant effects, in comparison to the C3-41 strain, are allocated upstream and downstream of the gene operons, we suggest that L. sphaericus CBAM5 may enclose different regulatory elements or non-coding sequences.

Chromosome structure

The origin of replication of the chromosome of L. sphaericus CBAM5 was estimated by similarities to several features of the corresponding regions in L. sphaericus C3-41, Bacillus sp. B-14905 and other close related bacteria, including colocalization of the genes: dnaA, dnaN, dnaX, recR and recF; and GC nucleotide skew [(G–C)/(G + C)] analysis. In the contig 19 (EWH31640:EWH31645) we found a typical cluster consisting of dnaA, dnaN, recF, gyrA and gyrB boxes. The predicted genes dnaB, dnaI, dnaG, dnaE, holA, holB, priAB, polA and recA were also found spread in the chromosomal and extrachosmomal sequences. The replication termination site of the chromosomal scaffold is believed to be localized near 2.92 Mbp in the contig 14. According to GC skew analysis, the coding bias for the two strands of the chromosome is for the majority of CDSs to be on the outer strand from 0 to ~2.92 Mbp, and on the inner strand from ~2.92 Mbp to the end of the chromosomal scaffold (contig 19, Figure 2). This was also confirmed by the presence of parC (EWH32537) and parE (EWH32538), which encode the subunits of the chromosome-partitioning enzyme topoisomerase IV. Similar to previous reports [50, 51], we did not find the homolog of rtp (replication terminator protein-encoding gene) in the chromosomal assembly of CBAM5.

Mobile elements

Lysinibacillus sphaericus CBAM5 displays 28 CDSs annotated as transposases, including three allocated in the extrachromosomal sequences. The most frequent families are IS1182, IS3 and IS4. In addition, four incomplete prophage regions were identified as follows: Thermus phage φOH2 (contig 12), Burkholderia phage ST79 (contig 14), and two regions comprising the Clostridium phage φSM101 (contigs 14 and 28). Prophage regions φOH2 and ST79 included putative encoding sequences for tail, lysis and baseplate proteins. None of the reported phages has been described in the Colombian strain L. sphaericus OT4b.31 [50].

Larvicidal toxins

The genome of L. sphaericus CBAM5 shows a wide repertoire of potential encoding sequences in terms of mosquitocidal toxins. In the contig 11, we found Mtx1 (EWH35097) and Mtx2 (EWH35034) CDSs located in an identical cluster as Hu et al. [51] described in the genome of L. sphaericus C3-41. This cluster includes two insertion sequences, one of them consisting of a disrupted transposase between the mtx1 and mtx2, as well. One Mtx3 CDSs (EWH32377) was found in contig 14. Upstream of this sequence, we could identify some IS3 family mobile elements and putative DeoR family transcriptional regulators. In addition, we found one hypothetical toxin from the family Mtx2 (PFam PF03318) in contig 11 (EWH35106) and a putative cereolysin O CDS (EWH31995) being described to be active against the German cockroach Blattela germanica
[52] in contig 15.

The binary toxin genes binA (EWH32662) and binB (EWH32663) of L. sphaericus CBAM5, which are the main source of its larvicidal activity [51], were found in the contig 14 following a similar arrangement as the 35-kb duplicate cluster of L. sphaericus C3-41 (Figure 4). Nearby the binA and binB genes, we found a putative Mtx2/3 toxin (EWH32665), two CDSs for phage integrases in the 5’ start of the 35-kb fragment. L. sphaericus CBAM5 also share a germination gene cluster equivalent to the B. anthracis plasmid pXO1 and the BinA/BinB cluster of L. sphaericus C3-41, having a GerXB-KA-XC gene cluster upstream of a transposase [51, 53]. Comparing the region comprised between the germination operon and the binA-binB genes across the sequences of L. sphaericus CBAM5, C3-41 and 2297, we found an equivalent homology of putative transposases with different length and disruption points. The strain CBAM5 has two mobile elements of 459 and 312 bp in length, which is similar to strains 2297 and CBAM5 showing a probable transposase pseudogene with 1,110 bp and 591 bp in length, respectively (Figure 4). As a final remark, in the 3’ end of the 35-kb fragment we found an incomplete encoding sequence for β-carotene 15,15’-monooxygenase probably disrupted by a mobile element (depicted with a red box in Figure 4). Hu et al. [51] hypothesized that the conserved 35-kb sequence, including the BinA, BinB, and the two phage integrase family proteins, are probably unique to the taxonomic L. sphaericus group 1 (formerly known as group IIA) being the remnant of a potential phage infection. Even though we cannot confirm the presence of additional BinA-B CDS sequences in the genome of L. sphaericus CBAM5, we suggest further research to confirm the participation of phage infections on the evolution of larvicidal toxins in the strain CBAM5.

Figure 4

Mosquitocidal binary toxin gene clusters ofL. sphaericusstrains CBAM5, C3-41 and 2297. Binary toxin BinA and BinB, Mtx2/3 homolog, CDSs for a phage integrase family protein, the GerXB-KA-XC operon, a ribonuclease, a putative peptide synthase, and a chitin-binding protein, hypothetical proteins (blue arrows) and transposases (gray arrows) are indicated. A 1554 bp insertion is located between the GerXB-KA-XC operon and BinA-B coding sequences. A disrupted CDS (red box) includes a mobile element and a hypothetical protein.

Surface (S) layer proteins and toxic metal resistances

L. sphaericus CBAM5 exhibits 21 CDSs described as surface (S) layer proteins or S-layer homologs in its genome. The fragment covered from EWH35069 to EWH35072 includes four CDSs encoding for a variable protein, a putative S-layer associated protein, a P60 invasion-associated protein and a N-acetylmuramoyl-L-alanine amidase. Probably the genes located in this fragment may participate in the larvicidal activity of the strain CBAM5, given that the same genes have been described as differentially expressed in virulent infections of Lysteria monocytogenes
[54]. A total of 14 CDSs show three SLHs motifs near to the N terminal region, similarly to the slpC gene previously described in native strains [5]. In addition, we found two S-layer surface array proteins in the chromosomal scaffold and another in extracromosomal sequences.

A total of 64 CDSs corresponded to encoding sequences involved in responses against toxic metal(oid)s. Among those coding sequences, we found the following operons: arsRBCDA, arsRBC, cadCA, mntABCD, nikABCDE, terD-terD-terD, zurR-znuBC, and czrA-czcD-csoR-copZA. We could identify various genes probably involved in metal(loid) resistances spread across the genome (Additional file 4: Table S2). The chrA gene seems to be the only representative of the chr operon in the genome of L. sphaericus CBAM5. Previous reports have shown that microorganisms bearing chrA homologues display highly variable resistance levels against Cr(VI) [55]. However, two superoxide dismutase putative proteins (EWH33050, EWH30224) and several CDS ascribed as flavin reductases (EC 1.5.1.29), nitroreductases (EC 1.5.1.34) and quinone reductases (EC 1.1.5.4) could cooperate in the Cr(VI) resistance, in agreement with previous reports [55, 56].

Given the heavy metal resistance of L. sphaericus CBAM5 in polluted environments, and supported by the identification of genes in Additional file 4: Table S2, we could expect the assistance of efflux pump systems and heavy-metal resistance proteins specific to As, Sb, Ni, Zn, Cu, Cd, Te, Cr, Mn and Co. By the evaluation of coalescent models, Villegas-Torres et al. [10] proposed that L. sphaericus CBAM5 may have acquired the arsC gene through recent events of horizontal gene transfer as a possible adaptation to polluted environments. However, we found highly similar homologues of heavy metal resistance proteins of the CBAM5 strain in microorganisms isolated from non-polluted environments (i.e. czrA-czcD-csoR-copZA, cadCA, and arsRBC in L sphaericus OT4B.31 [50]). Further analysis on plasmids, prophage content, or conjugation factors may clarify the origin of resistance (as well as larvicidal) genes. Finally, based in the KEGG analysis, some predicted proteins might participate in peripheral pathways for the degradation of geraniol, chlorocyclohexane, chlorobenzene, benzoate, bisphenol, fluorobenzoate, toluene, chloroalkane, chloroalkene, naphthalene, aminobenzoate, styrene, atrazine, limonene and pinene.

Lysinibacillus sphaericus CBAM5 was isolated from drilling mineral base oil samples at the subsurface soil level. By comparing the chromosomal sequences between L. sphaericus strains CBAM5 and C3-41, we identified distinctive similarities of the DNA homology group IIA. The evidence of the binary toxins allocated in a conserved cluster delimited by mobile elements, resembles a probable phage invasion in the DNA subgroup IIA of the Lysinibacillus sphaericus species. Along with the biological control potential given by the Mtx, Bin and cerolysin toxins, L. sphaericus CBAM5 displays encoding sequences for S-layer proteins and heavy-metal efflux pumps, which may confer resistance to As, Sb, Ni, Zn, Cu, Cd, Te, Cr, Mn and Co in polluted environments.

Acknowledgements

This work was performed under the auspices of the Grant 1204-452-21129 from the Instituto Colombiano para el fomento de la Investigación Francisco José de Caldas – Colciencias, the Research Fund from the Faculty of Sciences at Universidad de los Andes, and the Centro de Investigaciones Microbiológicas (CIMIC).

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